..PROSESS is intended to serve as a tool that can be used by structure biologists as well as database curators to assess and validate newly determined protein structures. PROSESS is freely available at http://www.prosess.ca...

..MSEA has the potential to help users identify obvious as well as 'subtle but coordinated' changes among a group of related metabolites that may go undetected with conventional approaches. MSEA is freely available at http://www.msea.ca...

..Gene, metabolite and protein concentration data can also be visualized through SMPDB's mapping interface. All of SMPDB's images, image maps, descriptions and tables are downloadable. SMPDB is available at: http://www.smpdb.ca...

T3DB: a comprehensively annotated database of common toxins and their targets

..On average, the correlation between RCI predictions and experimentally obtained motional amplitudes is within the range from 0.77 to 0.82. The server is available at http://wishart.biology.ualberta.ca/rci...

..Its f-measure on these tasks is 88, 81 and 79%, respectively. These values are between 5 and 50% better than other published tools. The server is freely available at http://wishart.biology.ualberta.ca/polysearch...

David S WishartDepartment of Computing Science, Department of Biological Sciences, University of Alberta and National Research Council, National Institute for Nanotechnology NINT, Edmonton, AB, Canada T6G 2E8Nucleic Acids Res 36:W496-502. 2008

..The performance of CS23D is dependent on the completeness of the chemical shift assignments and the similarity of the query protein to known 3D folds. CS23D is accessible at http://www.cs23d.ca...

..This performance is 10-20% better than what is typically obtained from standard 'ab initio' predictions. PPT-DB, its prediction utilities and all of its contents are available at http://www.pptdb.ca...

Scott MontgomerieDepartment of Computing Science and Department of Biological Sciences, University of Alberta and National Research Council, National Institute for Nanotechnology NINT, Edmonton, AB, Canada T6G 2E8Nucleic Acids Res 36:W202-9. 2008

..2 A RMSD). The average PROTEUS2 prediction takes approximately 3 min per query sequence. The PROTEUS2 server along with source code for many of its modules is accessible a http://wishart.biology.ualberta.ca/proteus2...

..0 represents the result of 2 years of manual annotation work aimed at making the database much more useful for a wide range of 'omics' (i.e. pharmacogenomic, pharmacoproteomic, pharmacometabolomic and even pharmacoeconomic) applications...

..METAGENassist also generates colorful, publication quality tables and graphs that can be downloaded and used directly in the preparation of scientific papers. METAGENassist is available at http://www.metagenassist.ca...

..PHAST also generates downloadable, high quality, interactive graphics that display all identified prophage components in both circular and linear genomic views. PHAST is available at (http://phast.wishartlab.com)...

..We hypothesized that a more efficient "partial" clustering approach in combination with an improved scoring scheme could significantly improve both the speed and performance of existing candidate selection methods...

..KS10 was isolated as a prophage of B. cenocepacia K56-2, a clinically relevant strain of the BCC. Our objective was to sequence the genome of this phage and also determine if this prophage encoded any virulence determinants...

..For proteins of known three-dimensional structure, their contact order can be calculated directly. However, for proteins with unknown three-dimensional structure, there is no effective prediction method currently available...

..Tables containing the compounds, concentrations, spectra, protocols and links to disease associations that we have found for the human CSF metabolome are freely available at http://www.csfmetabolome.ca...

..The strengths and limitations of these approaches as applied to different analytical technologies (GC-MS, LC-MS and NMR) will be discussed, as will prospects for potential improvements to existing strategies...

..Changes to the user-interface have also been implemented to accommodate future expansion and to make database navigation much easier. These improvements should make the HMDB much more useful to a much wider community of users...

..The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca...

Metabolomics: the principles and potential applications to transplantation

..These derived parameters can be used to rapidly identify both general and residue-specific problems within newly determined protein structures. The VADAR web server is freely accessible at http://redpoll.pharmacy.ualberta.ca/vadar...

..coli (strain K12). The database is self-updating but also supports 'community' annotation, and provides an extensive array of viewing, querying and search options including a powerful, easy-to-use relational data extraction system...

..The PA system produces a Naïve Bayes classifier, which is amenable to a graphical and interactive approach to explanations for its predictions; transparent predictions increase the user's confidence in, and understanding of, PA...

..The images and textual output are of sufficient quality that they may be used directly in publications or presentations. The PlasMapper web server is freely accessible at http://wishart.biology.ualberta.ca/PlasMapper...

Identification of predictive biomarkers of disease state in transition dairy cows

Mark BerjanskiiDepartment of Computing Science, University of Alberta and National Research Council, National Institute for Nanotechnology, Edmonton, AB, Canada T6G 2E8Nucleic Acids Res 37:W670-7. 2009

..GeNMR was developed to facilitate rapid, user-friendly structure determination of protein structures via NMR spectroscopy. GeNMR is accessible at http://www.genmr.ca...

Spatiotemporal integration of molecular and anatomical data in virtual reality using semantic mapping

..MetaboAnalyst is capable of handling most kinds of metabolomic data and was designed to perform most of the common kinds of metabolomic data analyses. MetaboAnalyst is accessible at http://www.metaboanalyst.ca...

..This chapter is intended to illustrate how bioinformatics and cheminformatics can work synergistically to help provide the necessary inputs for computer-aided drug design...

In silico drug exploration and discovery using DrugBank

David S WishartUniversity of Alberta and the National Institute of Nanotechnology NINT National Research Council, Edmonton, Alberta, CanadaCurr Protoc Bioinformatics . 2007

..The intent of this unit is to give readers some introduction into the field of cheminformatics (the study of chemical information) and to show how cheminformatics can be seamlessly integrated into the field of bioinformatics...

..thermoautotrophicum, while Mt0895 plays a minor or supportive role. We also suggest that these two molecules (Mt0807 and Mt0895) may represent a group of ancient proteins that were ancestral to both thioredoxins and glutaredoxins...

..This study assists in the understanding of structure-activity relationships in type IIa bacteriocins and demonstrates the importance of the conserved C-terminal amphipathic alpha helix for activity...

..Further, we show that this chemical shift method is able to quantitatively predict per-residue RMSD values (from both MD simulations and NMR structural ensembles) as well as model-free backbone order parameters...

Identification of a novel archaebacterial thioredoxin: determination of function through structure

..Furthermore, this protocol appears to improve the accuracy of chemical shift-derived secondary structural identification, and has been formally incorporated into a computer program called PSSI (http//www.pronmr.com)...

..We believe this information could be particularly useful for the prediction of beta-turn propensity, the development of peptide-based drugs, and the de novo design of peptides, proteins, and peptidyl mimetics...